[FieldTrip] A paper mentioned in "Non-parametric cluster-based > statistical testing of MEG/EEG data" video on FieldtripTV channel
Natalia Melnik
e163581 at gmail.com
Fri Mar 20 17:31:17 CET 2015
Yeah, it seems to be the paper! Thank you very much!
Cheers,
Natalia
On 20 March 2015 at 13:00, <fieldtrip-request at science.ru.nl> wrote:
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> Today's Topics:
>
> 1. Re: strange leadfield for beamforming from template files
> (Schoffelen, J.M. (Jan Mathijs))
> 2. Re: Easycap M10 coregistration with head model ? no fiducials
> (Herring, J.D. (Jim))
> 3. A paper mentioned in "Non-parametric cluster-based
> statistical testing of MEG/EEG data" video on FieldtripTV channel
> (Natalia Melnik)
> 4. Re: A paper mentioned in "Non-parametric cluster-based
> statistical testing of MEG/EEG data" video on FieldtripTV channel
> (Nicholas A. Peatfield)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 19 Mar 2015 21:18:38 +0000
> From: "Schoffelen, J.M. (Jan Mathijs)" <jan.schoffelen at donders.ru.nl>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] strange leadfield for beamforming from
> template files
> Message-ID: <47A755CA-A6B5-4B56-AD75-866D2329B4F7 at fcdonders.ru.nl>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Maurice,
> The way in which you visualize the leadfield vectors it is hard to see in which locations the arrows are big. My suspicion is (unless otherwise proven) that you are suffering from numerical problems at dipole positions close to the inner boundary.
> Best,
> Jan-Mathijs
>
>
>
> On Mar 19, 2015, at 12:34 PM, m.goeldi at psychologie.uzh.ch<mailto:m.goeldi at psychologie.uzh.ch> wrote:
>
>
> Hi all
>
> I am trying to do beamforming with my EEG data. I am using the template headmodel etc provided in fieldtrip to compute the leadfield.
> Since my data looks strange I have visualized the leadfield expecting grid points close to the electrode to have a larger leadfield.
> Unfortunately this is not the case. The vectors are all over the place. See figure.
>
>
> [X]
> The red circle is the electrode location (Cz).
> The field looks (qualitatively) just as wrong for any other electrode.
>
> Below is the code I used to generate & visualize the lead field.
>
> I have used the same code to visualize the leadfield from a example MEG file from the fieldtrip page.
> There the result is as expected, so I think the problem lies not in the visualization.
>
> I am using fieldtrip-20150118
>
> I have tried all the standard_sourcemodel3d*mm files. Qualitatively the error remains the same.
>
> My question is, am I doing anything wrong in generating the lead field?
> Am I expecting something wrong (i.e. is this a realistidc lead field?)
> Does anyones lead field look the same/different when using the template files?
>
> I would appreciate any help with this problem.
>
>
> Thanks for your thoughts
>
> Cheers
> Maurice
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
> % load mri
> load('C:\Program Files\MATLAB\fieldtrip-20150118\template\headmodel\standard_mri.mat')
>
> % load template sourcemodel
> template = load('C:\Program Files\MATLAB\fieldtrip-20150118\template\sourcemodel\standard_sourcemodel3d8mm');
>
> % compute source model
> cfg = [];
> cfg.grid.warpmni = 'yes';
> cfg.grid.template = template.sourcemodel;
> cfg.grid.nonlinear = 'yes'; % use non-linear normalization
> cfg.grid.resolution = 6;
> cfg.mri = mri;
> sourcemodel = ft_prepare_sourcemodel(cfg);
> sourcemodel = ft_convert_units(sourcemodel, 'cm');
>
> % make head model
> load('C:\Program Files\MATLAB\fieldtrip-20150118\template\headmodel\standard_bem.mat');
> vol = ft_convert_units(vol, 'cm');
>
> %% electrode layout
> elec = ft_read_sens('C:\Program Files\MATLAB\spm12\EEGtemplates\egi128_GSN_HydroCel.sfp');
> [elec] = removeelectrodes(elec,data.label); % remove the electrodes that are not in my data
> elec = ft_convert_units(elec,'cm');
>
> % lead field
> cfg = [];
> cfg.grid = sourcemodel;
> cfg.elec = elec;
> cfg.vol = vol;
> cfg.channel = 'all';
> [grid] = ft_prepare_leadfield(cfg,freqC1);
> grid = ft_convert_units(grid, 'cm');
>
>
>
> %%%% visualize leadfield %%%%
> channel = 'Cz';
>
> %% electrode position
> elecpos = grid.cfg.elec.elecpos(strcmp(grid.cfg.elec.label,channel),:);
>
> %% leadfield positions
> leadfieldpos = grid.pos(grid.inside,:);
>
> %% extract leadfield
> npts = numel(grid.leadfield);
> lead = grid.leadfield(grid.inside);
>
> nchan = find(strcmp(grid.cfg.channel,channel));
> for i = 1:numel(lead)
> leadVect(i,:) = lead{i}(nchan,:);
> end
>
> figure; hold on % plot all objects in one figure
> ft_plot_mesh(vol.bnd(3), 'edgecolor','none','facealpha',0.8,'facecolor',[0.6 0.6 0.8]);
> ft_plot_mesh(vol.bnd(2), 'edgecolor','none','facealpha',0.8,'facecolor','y');
> alpha 0.3
> scale = 30;
> quiver3(leadfieldpos(:,1),leadfieldpos(:,2),leadfieldpos(:,3),leadVect(:,1),leadVect(:,2),leadVect(:,3),scale)
> plot3(elecpos(1),elecpos(2),elecpos(3),'ro')
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
>
>
> ---
> University of Z?rich
> Maurice G?ldi
> Department of Psychology
> Biopsychology
> Binzm?hlestr. 14 / Box 5
> CH - 8050 Z?rich
>
> Tel. +41 (0)44 635 74 55
> www.psychologie.uzh.ch<http://www.psychologie.uzh.ch/>
> maurice.goeldi at uzh.ch<mailto:maurice.goeldi at uzh.ch>
> _______________________________________________
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> ------------------------------
>
> Message: 2
> Date: Fri, 20 Mar 2015 09:29:40 +0000
> From: "Herring, J.D. (Jim)" <j.herring at donders.ru.nl>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] Easycap M10 coregistration with head model ?
> no fiducials
> Message-ID:
> <3D00B7615FB58D46A0B49B9AD67A33EB1892CB at exprd01.hosting.ru.nl>
> Content-Type: text/plain; charset="windows-1252"
>
> Dear Milan,
>
> If you have not recorded the electrode positions yourself using, for example, a Polhemus or Localite system you will always end-up with a suboptimal alignment (fiducials, or not).
>
> That being said, you can skip the step of automatic realignment in the tutorial and immediately use ft_electroderealign with cfg.method = 'interactive', to manually rotate, translate, and scale the electrode positions to make it fit as well as possible to your headmodel.
>
> Best,
>
> Jim
> ________________________________
> From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Milan Mitka [mitka3 at uniba.sk]
> Sent: Wednesday, March 18, 2015 9:54 PM
> To: fieldtrip at science.ru.nl
> Subject: [FieldTrip] Easycap M10 coregistration with head model ? no fiducials
>
> Greetings,
>
> I'm having difficulties with aligning easycap M10 electrodes with a head model. I'm following this tutorial: http://fieldtrip.fcdonders.nl/tutorial/headmodel_eeg#align_the_electrodes
>
> The problem as I see it is that the file FieldTrip/template/electrode/easycap-M10.txt that I'm using istead of standard_1020.elc doesn't include fiducials and can therefore not be properly aligned with the head model automatically.
>
> How can I properly align M10 electrodes defined in spherical coordinates or convert MNI cartesian coordinates to the head model coordinates which appear to use CTF, please?
>
> Yours faithfully
> Milan Mitka
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> ------------------------------
>
> Message: 3
> Date: Fri, 20 Mar 2015 11:58:26 +0200
> From: Natalia Melnik <e163581 at gmail.com>
> To: fieldtrip at science.ru.nl
> Subject: [FieldTrip] A paper mentioned in "Non-parametric
> cluster-based statistical testing of MEG/EEG data" video on
> FieldtripTV channel
> Message-ID:
> <CAHphXiWKjs_kp-sEzFK=kaUo_VqZvsFC6rj7fQmhxvF-GMYwhw at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear all,
> in the "Non-parametric cluster-based statistical testing of MEG/EEG
> data" video on FieldtripTV channel
> ((https://youtu.be/vOSfabsDUNg?t=17m34s) ), Dr. Oostenveld mentiones
> (at 17:38) a paper which tested some of the parameters of the
> statistic methods. Do you know which paper is it?
>
> Cheers,
> Natalia.
>
>
> ------------------------------
>
> Message: 4
> Date: Fri, 20 Mar 2015 11:48:24 +0100
> From: "Nicholas A. Peatfield" <nick.peatfield at gmail.com>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] A paper mentioned in "Non-parametric
> cluster-based statistical testing of MEG/EEG data" video on
> FieldtripTV channel
> Message-ID:
> <CADzq99mxQEyS19zaq5HLXvHuGMkLg0hnXvZ7bB__BVOUa0mWWg at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Not sure if this is the one. But it seems as such:
>
> http://www.sciencedirect.com/science/article/pii/S0165027014002878
>
> Pernet, C.R., Latinus, M. <http://eprints.gla.ac.uk/view/author/9657.html>,
> Nichols, T.E., and Rousselet, G.A.
> <http://eprints.gla.ac.uk/view/author/5180.html> (2014) Cluster-based
> computational methods for mass univariate analyses of event-related brain
> potentials/fields: A simulation study. *Journal of Neuroscience Methods
> <http://eprints.gla.ac.uk/view/journal_volume/Journal_of_Neuroscience_Methods.html>*
> . (doi:
> <http://dx.doi.org/10.1016/j.jneumeth.2014.08.003%20%3Chttp://dx.doi.org/10.1016/j.jneumeth.2014.08.003%3E>
> 10.1016/j.jneumeth.2014.08.003
> <http://dx.doi.org/10.1016/j.jneumeth.2014.08.003>) (Early Online
> Publication)
>
>
>
> On 20 March 2015 at 10:58, Natalia Melnik <e163581 at gmail.com> wrote:
>
>> Dear all,
>> in the "Non-parametric cluster-based statistical testing of MEG/EEG
>> data" video on FieldtripTV channel
>> ((https://youtu.be/vOSfabsDUNg?t=17m34s) ), Dr. Oostenveld mentiones
>> (at 17:38) a paper which tested some of the parameters of the
>> statistic methods. Do you know which paper is it?
>>
>> Cheers,
>> Natalia.
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
>
> --
> Nicholas Peatfield, PhD
> Centro Interdipartimentale Mente/Cervello- CIMEC
> <http://www5.unitn.it/People/it/Web/Struttura/STO0008663>
> Assegnista di ricerca - Research Fellow
> Via delle Regole, 101 - 38060 Mattarello
> +39 0461 283086
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